Magnesium in PDB 6n99: Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1

All present enzymatic activity of Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1:
5.3.1.5;

The structure of Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1, PDB code: 6n99 was solved by R.Y.Miyamoto, P.S.Vieira, M.T.Murakami, L.M.Zanphorlin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.76 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	142.776, 82.293, 140.313, 90.00, 109.81, 90.00
R / Rfree (%)	26.7 / 31.6

The binding sites of Magnesium atom in the Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1 (pdb code 6n99). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1, PDB code: 6n99:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:43.8 occ:1.00 OD2 A:ASP257 2.1 47.1 1.0 OD2 A:ASP255 2.1 44.0 1.0 OE2 A:GLU217 2.5 44.6 1.0 CG A:ASP257 2.9 47.9 1.0 NE2 A:HIS220 3.1 43.3 1.0 CG A:ASP255 3.1 44.4 1.0 OD1 A:ASP257 3.2 47.6 1.0 CD A:GLU217 3.4 44.5 1.0 OD1 A:ASP255 3.4 45.0 1.0 OE1 A:GLU217 3.5 44.7 1.0 CE1 A:HIS220 3.8 43.0 1.0 CD2 A:HIS220 3.9 43.4 1.0 OD2 A:ASP287 4.1 50.1 1.0 NZ A:LYS183 4.3 45.1 1.0 CB A:ASP257 4.3 49.5 1.0 CB A:ASP255 4.4 44.4 1.0 ND2 A:ASN247 4.5 48.0 1.0 O A:ASP287 4.7 51.8 1.0 CG A:GLU217 4.8 44.1 1.0 NZ A:LYS289 4.8 48.0 1.0 ND1 A:HIS220 4.9 42.6 1.0 CG A:HIS220 4.9 42.8 1.0

Magnesium binding site 2 out of 5 in the Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:47.1 occ:1.00 OD2 B:ASP255 2.0 44.0 1.0 NE2 B:HIS220 2.3 46.0 1.0 OD1 B:ASP257 2.9 46.4 1.0 OE2 B:GLU217 3.0 47.3 1.0 CG B:ASP255 3.1 44.3 1.0 OE1 B:GLU217 3.1 47.3 1.0 CE1 B:HIS220 3.1 45.9 1.0 OD2 B:ASP257 3.3 46.3 1.0 CD2 B:HIS220 3.4 45.9 1.0 CD B:GLU217 3.4 47.3 1.0 CG B:ASP257 3.5 46.8 1.0 OD1 B:ASP255 3.6 45.0 1.0 NZ B:LYS183 3.9 45.5 1.0 ND1 B:HIS220 4.3 45.7 1.0 CB B:ASP255 4.3 44.1 1.0 OD2 B:ASP287 4.4 45.8 1.0 CG B:HIS220 4.4 45.6 1.0 CE B:LYS183 4.8 44.7 1.0 CG B:GLU217 4.9 47.6 1.0 ND2 B:ASN247 4.9 45.6 1.0 CD B:LYS183 4.9 44.6 1.0 CB B:ASP257 5.0 47.9 1.0

Magnesium binding site 3 out of 5 in the Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:51.2 occ:1.00 OD1 B:ASP245 2.3 47.5 1.0 OE2 B:GLU181 2.7 49.2 1.0 CG B:ASP245 3.1 47.1 1.0 OD2 B:ASP245 3.2 46.8 1.0 OD2 B:ASP287 3.4 45.8 1.0 ND2 B:ASN215 3.6 47.5 1.0 CD B:GLU181 3.6 48.3 1.0 CE B:MET88 3.7 46.9 1.0 NE2 B:HIS285 3.7 47.2 1.0 OE1 B:GLU181 3.9 48.0 1.0 CG B:ASP287 3.9 46.6 1.0 CD2 B:HIS285 4.1 47.4 1.0 CB B:ASP287 4.1 47.2 1.0 CZ2 B:TRP16 4.2 48.9 1.0 CB B:ASP245 4.5 47.1 1.0 CH2 B:TRP16 4.6 49.4 1.0 CE1 B:HIS285 4.7 48.0 1.0 CG B:ASN215 4.8 47.9 1.0 OD1 B:ASP287 4.8 46.9 1.0 CG1 B:VAL135 4.8 45.1 1.0 CG B:GLU181 5.0 47.7 1.0

Magnesium binding site 4 out of 5 in the Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:48.0 occ:1.00 OD2 C:ASP255 2.6 49.5 1.0 OE2 C:GLU217 2.8 51.0 1.0 OD2 C:ASP257 2.8 49.9 1.0 NE2 C:HIS220 3.1 50.3 1.0 OE1 C:GLU217 3.2 51.1 1.0 CD C:GLU217 3.4 51.3 1.0 CG C:ASP257 3.5 50.5 1.0 OD1 C:ASP257 3.6 50.4 1.0 CG C:ASP255 3.7 49.8 1.0 NZ C:LYS183 3.7 52.8 1.0 CE1 C:HIS220 3.8 50.2 1.0 NZ C:LYS289 4.0 55.5 1.0 CE C:LYS289 4.0 55.6 1.0 CD2 C:HIS220 4.2 50.3 1.0 OD2 C:ASP287 4.2 53.7 1.0 OD1 C:ASP255 4.3 50.5 1.0 CG C:ASP287 4.4 54.1 1.0 OD1 C:ASP287 4.5 53.9 1.0 O C:ASP287 4.6 55.0 1.0 CB C:ASP255 4.7 49.3 1.0 CB C:ASP257 4.9 51.3 1.0 CG C:GLU217 4.9 52.0 1.0 ND1 C:HIS220 4.9 50.3 1.0

Magnesium binding site 5 out of 5 in the Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:46.3 occ:1.00 OE1 D:GLU217 2.2 53.8 1.0 OD1 D:ASP255 2.3 52.0 1.0 OD2 D:ASP255 2.6 51.7 1.0 NE2 D:HIS220 2.6 51.3 1.0 OD1 D:ASP257 2.7 56.4 1.0 CG D:ASP255 2.8 52.2 1.0 CD D:GLU217 3.1 53.8 1.0 CD2 D:HIS220 3.3 51.1 1.0 OD2 D:ASP257 3.3 56.2 1.0 CG D:ASP257 3.3 56.7 1.0 OE2 D:GLU217 3.5 54.6 1.0 CE1 D:HIS220 3.6 50.3 1.0 ND2 D:ASN247 4.1 55.3 1.0 CB D:ASP255 4.3 52.8 1.0 OD1 D:ASP287 4.3 59.5 1.0 CG D:HIS220 4.4 49.9 1.0 CG D:GLU217 4.4 52.8 1.0 ND1 D:HIS220 4.5 49.5 1.0 NZ D:LYS183 4.5 49.0 1.0 CB D:ASP257 4.7 57.5 1.0 O D:ASP287 4.8 61.2 1.0 CE D:LYS183 5.0 48.1 1.0

R.Y.Miyamoto, A.S.De Souza, P.S.Vieira, R.R.De Melo, J.A.Scarpassa, C.H.I.Ramos, M.T.Murakami, R.Ruller, L.M.Zanphorlin. Xylose Isomerase 2F1 Variant From Streptomyces Sp. F-1 To Be Published.